[gmx-users] Protein-Ligand

[RAHUL SURESH]

Dear Justin
Thank you much.

About the term "curved", even am not exactly clear about it. Book by prof
Pamela states that sentence. As I feel she must be explaining about much
deformed protein.


On Tue, 16 May 2017 at 7:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/15/17 9:12 AM, RAHUL SURESH wrote:
> > Dear Users
> >
> > I am tryjng to simulate protein ligand complex using charmm36ff for
> 100ns.
> > I found the ligand moving away from the protein around 55ns. I don't
> think
> > it s a pbc effect. Is there anything I have done wrong or Should I add
> any
> > additional commands.?
> > Await your valuable advice.
> >
>
> Watch the trajectory and see which interactions break first.  Then
> consider if
> your ligand topology needs refinement to deal with such interactions or if
> it's
> trying to sample some strained conformation that is incompatible with
> binding
> (suggesting an internal/dihedral problem).  Compare with available
> experimental
> data; some things just have weak affinity.
>
> > PS: Will the ligand move out of protein if the protein is over curved
> after
> > interaction?
> >
>
> What does "over curved" mean?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*